[工程科技]Algorithmic challenges in computational molecular biophysics.pdfVIP

Journal of Computational Physics 151, 9–48 (1999) Article ID jcph.1998.6182, available online at on Algorithmic Challenges in Computational Molecular Biophysics Tamar Schlick, Robert D. Skeel, Axel T. Brunger,§ Laxmikant V. Kal´e, ¶ John A. Board, Jr., Jan Hermans, and Klaus Schulten Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and The Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012; Beckman Institute, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801-2987; §Department of Molecular Biophysics and Biochemistry, Yale University and The Howard Hughes Medical Institute, 266 Whitney Avenue, Bass Center, Room 434, New Haven, Connecticut 06520; Department of Electrical and Computer Engineering, Duke University, School of Engineering, Durham, North Carolina 27708; and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260 E-mail: schlick@, skeel@, §brunger@, ¶kale@, jab@, hermans@, kschulte@ Received August 20, 1998; revised December 11, 1998 A perspective of biomolecular simulations today is given, with illustrative appli- cations and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and recent descriptions of algorithmic work in long-time integration for molecular dynamics; fa