【摘 要】
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Fast Multipole Method(FMM)and Treecode are popular tree-based mul-tipole algorithms with rigorous error estimates and wide applications in computing N-body
【机 构】
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DepartmentofMathematics,SouthernMethodistUniversity,USA
【出 处】
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数学生物物理及分子生物学研讨会(The Mathematical Biophysics and Molecular Bi
论文部分内容阅读
Fast Multipole Method(FMM)and Treecode are popular tree-based mul-tipole algorithms with rigorous error estimates and wide applications in computing N-body particle interactions.FMM takes both near-field and far-field expansions,resulting in the revolutionary O(N)computations.Treecode takes only the far field expansion,receiving relatively less efficient O(N(logN))computations while gaining saved memory and improved parallelization efficiency for high performance comput-ing.This project first compares both methods under the Cartesian expansion in terms of efficiency,memory use,and parallel performance.Following that,the idea of the multipole expansion is used on a mesoscale chromatin model,in which the charge in-teractions cannot be uniformly accelerated using FMM or Treecode due to long-range cutoff,exclusion of local contacts,inhomogeneous particle distributions,specified in-teraction mechanisms,etc.The multipole expansion scheme on nucleosomes,the building blocks of the chromatin,circumvents the nonuniform difficulty to achieve significant speedup while maintains the flexibility of interactions.The scheme is used on both Monte Carlo sampling and Brownian Dynamics for the mesoscale chromatin model.
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