Literature DB >> 35821963

Artificial Intelligence for Accelerating Time Integrations in Multiscale Modeling.

Changnian Han1, Peng Zhang1,2, Danny Bluestein2, Guojing Cong3, Yuefan Deng1.   

Abstract

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%.

Entities:  

Keywords:  Adaptive time stepping; Artificial intelligence; Multiscale modeling; Platelet dynamics

Year:  2020        PMID: 35821963      PMCID: PMC9273111          DOI: 10.1016/j.jcp.2020.110053

Source DB:  PubMed          Journal:  J Comput Phys        ISSN: 0021-9991            Impact factor:   4.645


  19 in total

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Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-02-26

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Journal:  J Chem Phys       Date:  2009-10-21       Impact factor: 3.488

Review 3.  Multiscale modeling of biomolecular systems: in serial and in parallel.

Authors:  Gary S Ayton; Will G Noid; Gregory A Voth
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Review 4.  Biomolecular simulation: a computational microscope for molecular biology.

Authors:  Ron O Dror; Robert M Dirks; J P Grossman; Huafeng Xu; David E Shaw
Journal:  Annu Rev Biophys       Date:  2012       Impact factor: 12.981

5.  A Multiple Time Stepping Algorithm for Efficient Multiscale Modeling of Platelets Flowing in Blood Plasma.

Authors:  Peng Zhang; Na Zhang; Yuefan Deng; Danny Bluestein
Journal:  J Comput Phys       Date:  2015-03-01       Impact factor: 3.553

6.  Multiscale Modeling of Flow Induced Thrombogenicity With Dissipative Particle Dynamics and Molecular Dynamics.

Authors:  Danny Bluestein; João S Soares; Peng Zhang; Chao Gao; Seetha Pothapragada; Na Zhang; Marvin J Slepian; Yuefan Deng
Journal:  J Med Device       Date:  2014-04-28       Impact factor: 0.582

7.  A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps.

Authors:  Daniel T Margul; Mark E Tuckerman
Journal:  J Chem Theory Comput       Date:  2016-04-29       Impact factor: 6.006

8.  Scalability Test of Multiscale Fluid-Platelet Model for Three Top Supercomputers.

Authors:  Peng Zhang; Na Zhang; Chao Gao; Li Zhang; Yuxiang Gao; Yuefan Deng; Danny Bluestein
Journal:  Comput Phys Commun       Date:  2016-04-08       Impact factor: 4.390

9.  Multiscale coarse-graining of the protein energy landscape.

Authors:  Ronald D Hills; Lanyuan Lu; Gregory A Voth
Journal:  PLoS Comput Biol       Date:  2010-06-24       Impact factor: 4.475

10.  Simulation of platelets suspension flowing through a stenosis model using a dissipative particle dynamics approach.

Authors:  Joao S Soares; Chao Gao; Yared Alemu; Marvin Slepian; Danny Bluestein
Journal:  Ann Biomed Eng       Date:  2013-05-22       Impact factor: 3.934

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  1 in total

1.  Modeling of the thermal properties of SARS-CoV-2 S-protein.

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Journal:  Front Mol Biosci       Date:  2022-09-27
  1 in total

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