Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Lignin, a major component of lignocellulose, is the largest source of aromatic building blocks on the planet and harbors great potential to serve as starting material for the production of biobased products. Despite the initial challenges associated with the robust and irregular structure of lignin, the valorization of this intriguing aromatic biopolymer has come a long way: recently, many creative strategies emerged that deliver defined products via catalytic or biocatalytic depolymerization in good yields. The purpose of this review is to provide insight into these novel approaches and the potential application of such emerging new structures for the synthesis of biobased polymers or pharmacologically active molecules. Existing strategies for functionalization or defunctionalization of lignin-based compounds are also summarized. Following the whole value chain from raw lignocellulose through depolymerization to application whenever possible, specific lignin-based compounds emerge that could be in the fu...

Bright Side of Lignin Depolymerization: Toward New Platform Chemicals

Molecular modeling and simulations are invaluable tools for the polymer science and engineering community. These computational approaches enable predictions and provide explanations of experimentally observed macromolecular structure, dynamics, thermodynamics, and microscopic and macroscopic material properties. With recent advances in computing power, polymer simulations can synergistically inform, guide, and complement in vitro macromolecular materials design and discovery efforts. To ensure that this growing power of simulations is harnessed correctly, and meaningful results are achieved, care must be taken to ensure the validity and reproducibility of these simulations. With these considerations in mind, in this Perspective we discuss our philosophy for carefully developing or selecting appropriate models, performing, and analyzing polymer simulations. We highlight best practices, key challenges, and important advances in model development/selection, computational method choices, advanced sampling met...

Modeling and Simulations of Polymers: A Roadmap

https://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=1993&context=nanopub

Molecular dynamics predictions of thermal and mechanical properties of thermoset polymer EPON862/DETDA

This work presents a generalized structure generation methodology for amorphous polymers by a simulated polymerization technique and 21-step molecular dynamics equilibration, which is particularly effective for high-Tg polymers. The essential framework and parameters of the techniques and algorithms are described in detail, and example input scripts are provided for use with the freely available Polymatic simulated polymerization code and LAMMPS molecular dynamics package. The capabilities of the methods are examined through application to six linear, glassy polymers ranging in functionality, polarity, and rigidity. Validation of the methodology is provided by comparison of the simulations and experiments for a variety of structural, adsorption, and thermal properties, all of which showed excellent agreement with available experimental data.

Polymatic: a generalized simulated polymerization algorithm for amorphous polymers

Molecular simulations of crosslinking process of thermosetting polymers

This article reviews the field of molecular simula- tions of thermoset polymers. This class of polymers is of inter- est in applications ranging from structural components for aerospace to electronics packaging and predictive simulations of their response is playing an increasing role in understanding the molecular origin of their properties and complementing experiments in the search for tailored materials for specific applications. It focuses on modeling and simulation of the pro- cess of curing to predict the molecular structure of these poly- mers and their thermomechanical response by all-atom molecular dynamics simulations. Results from Monte Carlo and coarse-grained simulations are briefly summarized. V C 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 00, 000-000

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/polb.23489

Molecular scale simulations on thermoset polymers: A review

Molecular dynamics simulations and experimental studies of the thermomechanical response of an epoxy thermoset polymer

We use molecular dynamics simulations to characterize multilayer graphene reinforced epoxy composites. We focus on two configurations, one where the graphene layers are parallel to polymer/graphene interface and a perpendicular case, and characterize the in situ curing process of the resin and the thermo-mechanical response of the composites. The yield stress of the composites under uniaxial loading normal to the interface is in all cases larger than that of the bulk polymer even after the constraint of the reinforcement to transverse relaxation is taken into account. While both the parallel and normal configurations have very similar strengths, the parallel case exhibits cohesive yield with strain localization and nano-void formation within the bulk polymer while the case with graphene sheets oriented normal to the interface exhibit interfacial debonding. These two mechanisms lead to different post yield behavior and provide key insight for the development of predictive models of carbon fiber polymer composites.

/pdf/atomistic-simulations-on-multilayer-graphene-reinforced-fma341zbx2.pdf

Chunyu Li

Papers

Molecular dynamics predictions of thermal and mechanical properties of thermoset polymer EPON862/DETDA

Molecular simulations of crosslinking process of thermosetting polymers

Molecular scale simulations on thermoset polymers: A review

Molecular dynamics simulations and experimental studies of the thermomechanical response of an epoxy thermoset polymer

Atomistic simulations on multilayer graphene reinforced epoxy composites