Global optimization of morse clusters by potential energy transformations

被引:62
作者
Doye, JPK
Leary, RH
Locatelli, M
Schoen, F
机构
[1] Univ Cambridge, Chem Lab, Cambridge CB2 1EW, England
[2] Univ Calif San Diego, San Diego Supercomp Ctr, San Diego, CA 92186 USA
[3] Univ Turin, Dipartimento Informat, I-10149 Turin, Italy
[4] Univ Florence, Dipartimento Sistemi & Informat, I-50139 Florence, Italy
关键词
Morse potential; global optimization; basin-hopping; two-phase local search;
D O I
10.1287/ijoc.1040.0084
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
The Morse potential is a simple model for the potential energy of atoms with a single parameter p that determines the width of the potential well and allows a wide variety of materials to be modeled. Morse clusters are particularly important for applications, but their global optimization is also an extremely hard problem, highly relevant to methods that are to be applied to find the optimal configuration of a biomolecule. In particular, large p values are very challenging and, until now, no unbiased global-optimization method has been able to detect all the (putative) global minima at rho = 14 for clusters with up to N = 80 atoms. In this paper we introduce some techniques for transforming the original Morse potential that allow us to increase considerably the efficiency in locating the known global minima and also to discover some new optimal clusters. These methods are promising candidates for application to the optimization of biomolecules.
引用
收藏
页码:371 / 379
页数:9
相关论文
共 31 条
[1]   FREE-ENERGY LANDSCAPE FOR PROTEIN-FOLDING KINETICS - INTERMEDIATES, TRAPS, AND MULTIPLE PATHWAYS IN THEORY AND LATTICE MODEL SIMULATIONS [J].
ABKEVICH, VI ;
GUTIN, AM ;
SHAKHNOVICH, EI .
JOURNAL OF CHEMICAL PHYSICS, 1994, 101 (07) :6052-6062
[2]  
ADDIS B, 2003, 42003 DSI U STUD FIR
[3]   FUNNELS, PATHWAYS, AND THE ENERGY LANDSCAPE OF PROTEIN-FOLDING - A SYNTHESIS [J].
BRYNGELSON, JD ;
ONUCHIC, JN ;
SOCCI, ND ;
WOLYNES, PG .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 1995, 21 (03) :167-195
[4]   Modeling the structure of clusters of C60 molecules -: art. no. 235409 [J].
Doye, JPK ;
Wales, DJ ;
Branz, W ;
Calvo, F .
PHYSICAL REVIEW B, 2001, 64 (23) :2354091-23540911
[5]  
Doye JPK, 2001, FARADAY DISCUSS, V118, P159, DOI 10.1039/b0088811
[6]   Effect of compression on the global optimization of atomic clusters [J].
Doye, JPK .
PHYSICAL REVIEW E, 2000, 62 (06) :8753-8761
[7]   Structural consequences of the range of the interatomic potential - A menagerie of clusters [J].
Doye, JPK ;
Wales, DJ .
JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS, 1997, 93 (24) :4233-4243
[8]   Evolution of the potential energy surface with size for Lennard-Jones clusters [J].
Doye, JPK ;
Miller, MA ;
Wales, DJ .
JOURNAL OF CHEMICAL PHYSICS, 1999, 111 (18) :8417-8428
[9]   Thermodynamics of global optimization [J].
Doye, JPK ;
Wales, DJ .
PHYSICAL REVIEW LETTERS, 1998, 80 (07) :1357-1360
[10]   KINETICS OF PROTEIN-FOLDING - NUCLEATION MECHANISM, TIME SCALES, AND PATHWAYS [J].
GUO, ZY ;
THIRUMALAI, D .
BIOPOLYMERS, 1995, 36 (01) :83-102