Artificial intelligence for accelerating time integrations inmultiscale modeling

被引:19
作者
Han, Changnian [1 ]
Zhang, Peng [2 ]
Bluestein, Danny [2 ]
Cong, Guojing [3 ]
Deng, Yuefan [1 ]
机构
[1] SUNY Stony Brook, Dept Appl Math & Stat, Stony Brook, NY 11794 USA
[2] SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA
[3] IBM Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA
基金
美国国家卫生研究院;
关键词
Adaptive time stepping; Artificial intelligence; Multiscale modeling; Platelet dynamics; DISSIPATIVE PARTICLE DYNAMICS; MOLECULAR-DYNAMICS; MULTIPLE; PLATELETS; ALGORITHM; SYSTEMS; SCALES; SIMULATIONS;
D O I
10.1016/j.jcp.2020.110053
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
We developed a novel data-driven Artificial Intelligence-enhanced Adaptive Time Stepping algorithm (AI-ATS) that can adapt timestep sizes to underlying biophysical dynamics. We demonstrated its values in solving a complex biophysical problem, at multiple spatiotemporal scales, that describes platelet dynamics in shear blood flow. In order to achieve a significant speedup of this computationally demanding problem, we integrated a framework of novel AI algorithms into the solution of the platelet dynamics equations. Our framework involves recurrent neural network-based autoencoders by the Long Short-Term Memory and the Gated Recurrent Units as the first step for memorizing the dynamic states in long-term dependencies for the input time series, followed by two fully-connected neural networks to optimize timestep sizes and step jumps. The computational efficiency of our AI-ATS is underscored by assessing the accuracy and speed of a multiscale simulation of the platelet with the standard time stepping algorithm (STS). By adapting the timestep size, our AI-ATS guides the omission of multiple redundant time steps without sacrificing significant accuracy of the dynamics. Compared to the STS, our AI-ATS achieved a reduction of 40% unnecessary calculations while bounding the errors of mechanical and thermodynamic properties to 3%. (C) 2020 Elsevier Inc. All rights reserved.
引用
收藏
页数:17
相关论文
共 45 条
[21]  
Hochreiter S, 1997, NEURAL COMPUT, V9, P1735, DOI [10.1162/neco.1997.9.8.1735, 10.1162/neco.1997.9.1.1, 10.1007/978-3-642-24797-2]
[22]   A MULTIPLE-TIME-STEP MOLECULAR-DYNAMICS ALGORITHM FOR MACROMOLECULES [J].
HUMPHREYS, DD ;
FRIESNER, RA ;
BERNE, BJ .
JOURNAL OF PHYSICAL CHEMISTRY, 1994, 98 (27) :6885-6892
[24]   Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps [J].
Leimkuhler, Ben ;
Margul, Daniel T. ;
Tuckerman, Mark E. .
MOLECULAR PHYSICS, 2013, 111 (22-23) :3579-3594
[25]   A THEORY FOR MULTIRESOLUTION SIGNAL DECOMPOSITION - THE WAVELET REPRESENTATION [J].
MALLAT, SG .
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 1989, 11 (07) :674-693
[26]   A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps [J].
Margul, Daniel T. ;
Tuckerman, Mark E. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2016, 12 (05) :2170-2180
[27]   Long time molecular dynamics for enhanced conformational sampling in biomolecular systems [J].
Minary, P ;
Tuckerman, ME ;
Martyna, GJ .
PHYSICAL REVIEW LETTERS, 2004, 93 (15) :150201-1
[28]   Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances [J].
Morrone, Joseph A. ;
Markland, Thomas E. ;
Ceriotti, Michele ;
Berne, B. J. .
JOURNAL OF CHEMICAL PHYSICS, 2011, 134 (01)
[29]   FAST PARALLEL ALGORITHMS FOR SHORT-RANGE MOLECULAR-DYNAMICS [J].
PLIMPTON, S .
JOURNAL OF COMPUTATIONAL PHYSICS, 1995, 117 (01) :1-19
[30]  
Pothapragada S., 2015, INT J NUMER METH BIO, V31, P1