Perspective on coarse-graining, cognitive load, and materials simulation

Abstract The predictive capabilities of computational materials science today derive from overlapping advances in simulation tools, modeling techniques, and best practices. We outline this ecosystem of molecular simulations by explaining how important contributions in each of these areas have fed into each other. The combined output of these tools, techniques, and practices is the ability for researchers to advance understanding by efficiently combining simple models with powerful software. As specific examples, we show how the prediction of organic photovoltaic morphologies have improved by orders of magnitude over the last decade, and how the processing of reacting epoxy thermosets can now be investigated with million-particle models. We discuss these two materials systems and the training of materials simulators through the lens of cognitive load theory. For students, the broad view of ecosystem components should facilitate understanding how the key parts relate to each other first, followed by targeted exploration. In this way, the paper is organized in loose analogy to a coarse-grained model: The main components provide basic framing and accelerated sampling from which deeper research is better contextualized. For mentors, this paper is organized to provide a snapshot in time of the current simulation ecosystem and an on-ramp for simulation experts into the literature on pedagogical practice.

[1]  Vijay S Pande,et al.  Building Force Fields: An Automatic, Systematic, and Reproducible Approach. , 2014, The journal of physical chemistry letters.

[2]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[3]  Rajeev Kumar,et al.  New insights into the dynamics and morphology of P3HT:PCBM active layers in bulk heterojunctions. , 2013, Physical chemistry chemical physics : PCCP.

[4]  G. Voth Coarse-Graining of Condensed Phase and Biomolecular Systems , 2008 .

[5]  Stephen Thomas,et al.  New Methods for Understanding and Controlling the Self-Assembly of Reacting Systems Using Coarse-Grained Molecular Dynamics , 2018 .

[6]  Andrew L. Ferguson,et al.  Machine learning and data science in soft materials engineering , 2018, Journal of physics. Condensed matter : an Institute of Physics journal.

[7]  José Mario Martínez,et al.  PACKMOL: A package for building initial configurations for molecular dynamics simulations , 2009, J. Comput. Chem..

[8]  D. S. Perry,et al.  Improved force field for molecular modeling of poly(3-hexylthiophene). , 2013, The journal of physical chemistry. B.

[9]  Ian M. Mitchell,et al.  Best Practices for Scientific Computing , 2012, PLoS biology.

[11]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[12]  Arieh Warshel,et al.  Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. , 2011, Annual review of physical chemistry.

[13]  M. Baskes,et al.  Semiempirical, Quantum Mechanical Calculation of Hydrogen Embrittlement in Metals , 1983 .

[14]  Pak Lui,et al.  Strong scaling of general-purpose molecular dynamics simulations on GPUs , 2014, Comput. Phys. Commun..

[15]  Peter T. Cummings,et al.  Formalizing atom-typing and the dissemination of force fields with foyer , 2018, Computational Materials Science.

[16]  C. Steele,et al.  Ambient belonging: how stereotypical cues impact gender participation in computer science. , 2009, Journal of personality and social psychology.

[17]  H. Sun,et al.  COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds , 1998 .

[18]  F. Phelan,et al.  Quantitative Comparison of Atomistic Simulations with Experiment for a Cross-Linked Epoxy: A Specific Volume–Cooling Rate Analysis , 2018 .

[19]  D. Schwartz,et al.  A coarse grain model for DNA. , 2007, The Journal of chemical physics.

[20]  P. Khalatur,et al.  Highly Cross-Linked Epoxy Resins: An Atomistic Molecular Dynamics Simulation Combined with a Mapping/Reverse Mapping Procedure , 2007 .

[21]  Á. Lédeczi,et al.  Enabling Cross-Domain Collaboration in Molecular Dynamics Workflows , 2014 .

[22]  M. Baker 1,500 scientists lift the lid on reproducibility , 2016, Nature.

[23]  F. Chang,et al.  Phase Separation Process in Poly(-caprolactone)-Epoxy Blends , 1999 .

[24]  K. Daoulas,et al.  Generic Model for Lamellar Self-Assembly in Conjugated Polymers: Linking Mesoscopic Morphology and Charge Transport in P3HT , 2019, Macromolecules.

[25]  Thomas E. Gartner,et al.  Modeling and Simulations of Polymers: A Roadmap , 2019, Macromolecules.

[26]  Samin Ishtiaq,et al.  Reproducibility in Research: Systems, Infrastructure, Culture , 2015 .

[27]  Daniel R. Reid,et al.  SSAGES: Software Suite for Advanced General Ensemble Simulations. , 2018, The Journal of chemical physics.

[28]  Christian Trott,et al.  LAMMPScuda - a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses , 2012 .

[29]  Yong Zhang,et al.  PyLAT: Python LAMMPS Analysis Tools , 2019, J. Chem. Inf. Model..

[30]  David N. LeBard,et al.  Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing units , 2012 .

[31]  M. Wyer,et al.  Scientist Spotlight Homework Assignments Shift Students’ Stereotypes of Scientists and Enhance Science Identity in a Diverse Introductory Science Class , 2016, CBE life sciences education.

[32]  Aleksandra Pawlik,et al.  Data Carpentry: Workshops to Increase Data Literacy for Researchers , 2015 .

[33]  A. Stukowski Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool , 2009 .

[34]  V. Pande,et al.  Markov State Models: From an Art to a Science. , 2018, Journal of the American Chemical Society.

[35]  David L. Mobley,et al.  Best Practices for Foundations in Molecular Simulations [Article v1.0]. , 2019, Living journal of computational molecular science.

[36]  C. Groves,et al.  Simulating charge transport in organic semiconductors and devices: a review , 2017, Reports on progress in physics. Physical Society.

[37]  Tim Chartier,et al.  The Model Thinker: What You Need to Know to Make Data Work for You , 2019, Math Horizons.

[38]  Alejandro Strachan,et al.  Molecular scale simulations on thermoset polymers: A review , 2015 .

[39]  Jacob R. Gissinger,et al.  Chemical Reactions in Classical Molecular Dynamics. , 2017, Polymer.

[40]  A. V. Duin,et al.  ReaxFF: A Reactive Force Field for Hydrocarbons , 2001 .

[41]  Alberto Salleo,et al.  Structural Factors That Affect the Performance of Organic Bulk Heterojunction Solar Cells , 2013 .

[42]  Eric Jankowski,et al.  Optimization and Validation of Efficient Models for Predicting Polythiophene Self-Assembly , 2018, Polymers.

[43]  R. Dror,et al.  Long-timescale molecular dynamics simulations of protein structure and function. , 2009, Current opinion in structural biology.

[44]  Cheng-Kuang Lee,et al.  Multiscale molecular simulations of the nanoscale morphologies of P3HT:PCBM blends for bulk heterojunction organic photovoltaic cells , 2011 .

[45]  M. Moreno,et al.  Molecular modeling of crystalline alkylthiophene oligomers and polymers. , 2010, The journal of physical chemistry. B.

[46]  Vanessa Sochat,et al.  Singularity: Scientific containers for mobility of compute , 2017, PloS one.

[47]  Stefan Wagner,et al.  Poster: Communication in Open-Source Projects–End of the E-mail Era? , 2018, 2018 IEEE/ACM 40th International Conference on Software Engineering: Companion (ICSE-Companion).

[48]  V. Mavrantzas,et al.  All-Atom Molecular Dynamics Simulation of Temperature Effects on the Structural, Thermodynamic, and Packing Properties of the Pure Amorphous and Pure Crystalline Phases of Regioregular P3HT , 2013 .

[49]  A. Kolinski,et al.  Coarse-Grained Protein Models and Their Applications. , 2016, Chemical reviews.

[50]  H. Ibarra Provisional Selves: Experimenting with Image and Identity in Professional Adaptation , 1999 .

[51]  Samer Faraj,et al.  Why Should I Share? Examining Social Capital and Knowledge Contribution in Electronic Networks of Practice , 2005, MIS Q..

[52]  Jenessa R. Shapiro,et al.  The Role of Stereotype Threats in Undermining Girls’ and Women’s Performance and Interest in STEM Fields , 2012 .

[53]  Carla E. Estridge,et al.  Routine million-particle simulations of epoxy curing with dissipative particle dynamics , 2018 .

[54]  Z. Zhang,et al.  Multiscale Simulation Study on the Curing Reaction and the Network Structure in a Typical Epoxy System , 2011 .

[55]  Li Guo,et al.  Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics. , 2013, Journal of molecular graphics & modelling.

[56]  Georg von Krogh,et al.  Open Source Software and the "Private-Collective" Innovation Model: Issues for Organization Science , 2003, Organ. Sci..

[57]  C. Groves,et al.  Relating Molecular Morphology to Charge Mobility in Semicrystalline Conjugated Polymers , 2016 .

[58]  Nancy Wilkins-Diehr,et al.  Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained , 2018, Computing in Science & Engineering.

[59]  Daniel S. Katz,et al.  Report on the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4) , 2017, ArXiv.

[60]  David Beljonne,et al.  Energetics of Electron–Hole Separation at P3HT/PCBM Heterojunctions , 2013 .

[61]  M Scott Shell,et al.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems. , 2008, The Journal of chemical physics.

[62]  Jason D. Perlmutter,et al.  Mechanisms of virus assembly. , 2014, Annual review of physical chemistry.

[63]  B. Alder,et al.  Phase Transition for a Hard Sphere System , 1957 .

[64]  Thomas J Lane,et al.  MDTraj: a modern, open library for the analysis of molecular dynamics trajectories , 2014, bioRxiv.

[65]  Roland Faller,et al.  Coarse-Grained Computer Simulations of Polymer/Fullerene Bulk Heterojunctions for Organic Photovoltaic Applications. , 2010, Journal of chemical theory and computation.

[66]  Klaus Schulten,et al.  GPU-accelerated molecular modeling coming of age. , 2010, Journal of molecular graphics & modelling.

[67]  C. Luscombe,et al.  The Future of Organic Photovoltaics , 2015 .

[68]  Shawn A. Bohner,et al.  Model-Based Engineering of Software: Three Productivity Perspectives , 2009, 2009 33rd Annual IEEE Software Engineering Workshop.

[69]  Michelle Cook Visual representations in science education: The influence of prior knowledge and cognitive load theory on instructional design principles , 2006 .

[70]  Marsha C. Lovett,et al.  How learning works , 2010 .

[71]  Greg Wilson,et al.  Software Carpentry: lessons learned , 2014, F1000Research.

[72]  Chris Groves,et al.  Developing understanding of organic photovoltaic devices: kinetic Monte Carlo models of geminate and non-geminate recombination, charge transport and charge extraction , 2013 .

[73]  Austin Cory Bart,et al.  PythonSneks: An Open-Source, Instructionally-Designed Introductory Curriculum with Action-Design Research , 2019, SIGCSE.

[74]  Massimiliano Bonomi,et al.  PLUMED 2: New feathers for an old bird , 2013, Comput. Phys. Commun..

[75]  G. Grest,et al.  Dynamics of entangled linear polymer melts: A molecular‐dynamics simulation , 1990 .

[76]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[77]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[78]  Vyas Ramasubramani,et al.  signac - A Simple Data Management Framework , 2016, ArXiv.

[79]  M Scott Shell,et al.  Relative entropy as a universal metric for multiscale errors. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[80]  Cecilia Clementi,et al.  Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.

[81]  R. Faller,et al.  Modeling organic electronic materials: bridging length and time scales , 2017 .

[82]  D. Tieleman,et al.  Perspective on the Martini model. , 2013, Chemical Society reviews.

[83]  Clare McCabe,et al.  Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion. , 2014, The Journal of chemical physics.

[84]  Shantanu Singh,et al.  How Not To Drown in Data: A Guide for Biomaterial Engineers. , 2017, Trends in biotechnology.

[85]  J. Ponder,et al.  Force fields for protein simulations. , 2003, Advances in protein chemistry.

[86]  Oliver Beckstein,et al.  MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations , 2016, SciPy.

[87]  Markus Hösel,et al.  Solar cells with one-day energy payback for the factories of the future , 2012 .

[88]  Eric Jankowski,et al.  Enhanced Computational Sampling of Perylene and Perylothiophene Packing with Rigid-Body Models , 2017, ACS omega.

[89]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[90]  Chunyu Li,et al.  Molecular dynamics simulations and experimental studies of the thermomechanical response of an epoxy thermoset polymer , 2012 .

[91]  Samuel J. Keasler,et al.  Transferable potentials for phase equilibria-united atom description of five- and six-membered cyclic alkanes and ethers. , 2012, The journal of physical chemistry. B.

[92]  Florian Müller-Plathe,et al.  The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution. , 2015, The Journal of chemical physics.

[93]  Eric Jankowski,et al.  Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology , 2017 .

[94]  Cristian Hofmann,et al.  Integrating cognitive load theory and concepts of human-computer interaction , 2010, Comput. Hum. Behav..

[95]  T. Halgren,et al.  Polarizable force fields. , 2001, Current opinion in structural biology.

[96]  Daan Frenkel,et al.  Simulations: The dark side , 2012, The European Physical Journal Plus.

[97]  Nancy Wilkins-Diehr,et al.  XSEDE: Accelerating Scientific Discovery , 2014, Computing in Science & Engineering.

[98]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[99]  K. Binder,et al.  Dynamics of Collective Fluctuations and Brownian Motion in Polymer Melts , 1981 .

[100]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

[101]  D. Kahneman,et al.  Attention and Effort , 1973 .

[102]  Lanyuan Lu,et al.  Fitting coarse-grained distribution functions through an iterative force-matching method. , 2013, The Journal of chemical physics.

[103]  Daniel M. Oppenheimer Consequences of erudite vernacular utilized irrespective of necessity: problems with using long words needlessly , 2006 .

[104]  Peng Sun,et al.  Compact planar monopole antenna with ground branch for GSM/DCS/PCS/IMT2000 operation , 2006 .

[105]  Michael R Shirts,et al.  Testing for physical validity in molecular simulations , 2018, PloS one.

[106]  Jenn-Huei Lii,et al.  An improved force field (MM4) for saturated hydrocarbons , 1996, J. Comput. Chem..

[107]  D. Andrienko,et al.  Comparison of systematic coarse-graining strategies for soluble conjugated polymers , 2016 .

[108]  Tracey M. Clarke,et al.  Charge photogeneration in organic solar cells. , 2010, Chemical reviews.

[109]  Dirk Merkel,et al.  Docker: lightweight Linux containers for consistent development and deployment , 2014 .

[110]  Eric Jankowski,et al.  Computationally Linking Molecular Features of Conjugated Polymers and Fullerene Derivatives to Bulk Heterojunction Morphology , 2013 .

[111]  Ron Elber,et al.  Long-timescale simulation methods. , 2005, Current opinion in structural biology.

[112]  E. Peters,et al.  Multi-scale simulations for predicting material properties of a cross-linked polymer , 2015 .

[113]  Travis W. Kemper,et al.  Simplified Models for Accelerated Structural Prediction of Conjugated Semiconducting Polymers , 2017 .