A Conversation on The Fourth Industrial Revolution: Opportunities & Trends for Particle Based Simulation

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Abstract

In the margins of a recent multiscale simulation workshop a discussion began between a prominent  pharmaceutical industry scientist, and E-CAM and EMMC regarding the unfolding Fourth Industrial Revolution and the role of particle based simulation and statistical methods there.  The impact of simulation  is predicted to become very significant.  This discussion is intended to create awareness of the general public, of how industry 4.0 is initiating in companies, and  how academic research will support that transformation.

Authors: Prof. Pietro Asinari (EMMC and Politecnico di Torino, denoted below as PA) and Dr. Donal MacKernan (E-CAM and University College Dublin, denoted below as  DM) , and a prominent  pharmaceutical industry scientist (name withheld at author’s request as  the view expressed is a personal one, denoted below as  IS)

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E-CAM Case Study: Mesoscale models for polarisable solvents: application to oil-water interfaces

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Dr. Silvia Chiacchiera, Science and Technology Facilities Council, United Kingdom

Abstract

Water is a polar liquid and has a dielectric permittivity much higher than typical apolar liquids, such as light oils. This strong dielectric contrast at water-oil interfaces affects electrostatics and is important, for example, to include these effects to describe biomolecular processes and water-oil mixtures involving surfactants, as detergents. In this pilot project, developed in collaboration with Unilever and Manchester University, we have proposed and analysed a class of polarisable solvent models to be used in Dissipative Particle Dynamics (DPD), a coarse-grained particle-based simulation method commonly used in various industrial sectors. Related software modules for the DL_MESO package have also been developed.

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The Curse of Dimensionality in Data-Intensive Modeling in Medicine, Biology, and Diagnostics

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With Prof. Tim Conrad (TC), Free University of Berlin, and Dr. Donal Mackernan (DM), University College Dublin.

Abstract

Until recently the idea that methods rooted in statistical physics could be used to elucidate phenomena and underlying mechanisms in biology and medicine was widely considered to be a distant dream.  Elements of that dream are beginning to be realized, aided very considerably by machine learning and advances in measurement, exemplified by the development of large-scale biomedical data analysis for next-generation diagnostics. In this E-CAM interview of Tim Conrad,  the growing importance of diagnostics in medicine and biology is discussed. One difficulty faced by such developments and shared with particle-based simulation is the “curse of dimensionality”. It is manifest in problems such as: (a) the use of a very large number of order parameters when trying to identify reaction mechanisms, nucleation pathways, metastable states, reaction rates; polymorph recognition (b) machine learning  applied to electronic structure  problems – such as neural network based potentials need very high dimensional basis sets; (c) systematic coarse-graining would ideally start with a very high dimensional space and systematically reduce the dimension.  The opportunities and challenges for scientists engaging with industry are also discussed. Tim Conrad is Professor of “Medical Bioinformatics” at the Institute of Mathematics of the Free University of Berlin and head of MedLab, one of the four laboratories of the Modal research campus. MODAL is a public-private partnership project which conducts mathematical research on data-intensive modeling, simulation, and optimization of complex processes in the fields of energy, health, mobility, and communication.  Tim Conrad is also the founder of three successful start-up companies.

In this E-CAM interview with Prof. Tim Conrad, the growing importance of diagnostics in medicine and biology is discussed, including concepts rooted in signal analysis relevant to systematic dimensional reduction, and pattern recognition, and the possibilities of their application to systematic coarse-graining. The opportunities and challenges for scientists of start-up companies are also discussed based on experience.

 

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Scientific reports from the 2018 E-CAM workshops are now available on our website

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The scientific reports* from the following workshops conducted in year 3 of the project E-CAM (2018):

  1. E-CAM Scoping Workshop: “Solubility prediction”, 14 – 15 May 2018, Ecole Normale Supérieure de Lyon, France,
  2. E-CAM Scoping Workshop: “Dissipative particle dynamics: Where do we stand on predictive application?”, 24 – 26 April 2018, Daresbury Laboratory, United Kingdom,
  3. E-CAM Extended Software Development Workshop 11: “Quantum Dynamics”, 18 – 29 June 2018, Maison de la Simulation, France,

are now available for download on our website at this location. Furthermore, they will also be integrated in the CECAM Report of Activities for 2018, published every year on the website www.cecam.org.

 

*© CECAM 2018, all rights reserved.

Please address any comments or questions to info@e-cam2020.eu.

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Improving I/O of DL_MESO_DPD files using SIONlib

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This module implements the SIONlib library to optimize the I/O (writing/reading) of the trajectory files generated by DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package. SIONlib is a library for writing and reading binary data to/from several thousands of processors into one or a small number of physical files. For parallel access to files, only the open and close functions are collective, while the writing and reading of files can be done asynchronously. [1] In DL_MESO_DPD’s last release (version 2.6), the MPI version of DL_MESO_DPD generates multiple trajectory files, one for each MPI task. The interface with SIONlib optimizes the data writing so that just one physical file is produced from several MPI tasks. This drastic reduction in the number of output files is a benefit for the I/O of the code, and simplifies the maintenance of the output, especially for a large number of MPI tasks.

This module is part of the newly developed utilities for the DL_MESO_DPD code within the pilot project on Polarizable Mesoscale Models.

Practical application and exploitation of the code

The implementation of this module generates a single trajectory file (history.sion) in a parallel run of DL_MESO_DPD, instead of multiple (HISTORY) ones. Accordingly, analogous modifications have to be implemented in the post-processing utilities that read the HISTORY files. As an example, the changes were implemented in a formatting utility. Besides showing how to adapt the reading, this allows a robust check of the implementation, since the output is human readable, contains the full trajectories, and can be readily compared with outputs obtained using the standard version of DL_MESO_DPD.

The next released version of DL_MESO_DPD (in development) will tackle the writing of files differently, producing a single trajectory file from the start. However, the interface proposed here provides this feature to the users of version 2.6, and represents an alternative solution for the handling of the trajectories.

It should be noted that this implementation is meant to show the feasibility of the interfacing, not to deal with all the possible cases. Thus, the module’s functionality is restricted to the relevant case in which: i) the simulation is run in parallel using MPI, ii) a single SIONlib-type physical file is produced, and iii) the post-processing is done by a single process.

While SIONlib is optimized for a large number of MPI tasks, even the reduction from several output files to just one represents a benefit, for example when it comes to the maintenance of the simulation output.

 

[1] http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html

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New publication is out: “Adaptive Resolution Molecular Dynamics Technique: Down to the Essential”

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A new publication by the Theoretical and Mathematical Physics in Molecular Simulation group of the Freie Universität Berlin, lead by Prof. Luigi Delle Site, E-CAM partner, was published in the Journal of Chemical Physics. In it, the authors study the application of the thermodynamic force in the coupling region of an adaptive resolution molecular dynamics simulation (AdResS) approach which assures thermodynamic equilibrium and proper exchange of molecules between atomistically resolved and coarse-grained regions.

The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher AIP version can be found at https://doi.org/10.1063/1.5031206.

This work was performed in the context of the E-CAM pilot project on the development of the GC-AdResS scheme, which is a collaboration with MODAL AG. One of its goals is to develop a library or recipe with which GC-AdResS can be implemented in any MD Code. The current focus is to adjust the implemented version of GC-AdResS in GROMACS. The long-term goal of this project is to promote and stimulate the community to use it as a tool for multiscale simulations and analysis. More information about this pilot project can be found here.

Article

Title: Adaptive Resolution Molecular Dynamics Technique: Down to the Essential

Authors: Christian Krekeler, Animesh Agarwal, Christoph Junghans, Matej Praprotnik, Luigi Delle Site

Abstract: We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region.

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E-CAM Case Study: The implementation of a hierarchical equilibration strategy for polymer melts, to help studying the rheological properties of new composite materials

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Dr. Hideki Kobayashi, Max-Planck-Institut für Polymerforschung, Germany

Abstract

The ability to accurately determine and predict properties of newly developed polymer materials is highly important to researchers and industry, but at the same time represents a significant theoretical and computational challenge. We have developed a novel multiscale simulation method based on the hierarchical equilibration strategy, which significantly decreases the equilibrium properties calculation time while satisfying the thermodynamic consistency. A number of E-CAM modules was developed and implemented in he ESPResSo++ software package.

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Coarse-Graining module, a Component of the Hierarchical Equilibration Strategy for Polymer Melts

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To study the properties of polymer melts by numerical simulations, equilibrated configurations must be prepared. However, the relaxation time for high molecular weight polymer melts is huge and increases, according to reptation theory, with the third power of the molecular weight. Hence, an effective method for decreasing the equilibration time is required. The hierarchical strategy pioneered in Ref. [1] is a particularly suitable way to do this. The present module provides a part of that method.

To decrease the relaxation time, microscopic monomers are coarse-grained (CG) by mapping each subchain with N_{b} monomers onto a soft blob. The CG system is then characterized by a much lower molecular weight and thus is equilibrated quickly. The present module provides a python script which performs this coarse-graining procedure. The implementation details can be seen in the module’s documentation on our software Library here. This module is part of a set of codes that together implement the Hierarchical Equilibration strategy of Ref. [1], in the ESPResSO++ [2] (for the complete list of modules, see here under ESPResSO++).

 

Practical application and exploitation of the code

The development of a multiscale method for polymer blends and block copolymers is fundamentally new and needs to be based on first-principles theory. This is therefore an intellectual challenge in its own right. Furthermore, this paves the way to analyze the physical properties of novel composite materials that attract the attention of industrial companies. Such materials may be promising ingredients of new products like e.g. efficient and environment-friendly car tires. The implementation of the Hierarchical Equilibration strategy in the ESPResSO++ package is a step towards achieving this goal. In particular,  the practical application of this strategy is the E-CAM pilot project in collaboration with Michelin aimed at studying the Rheological Properties of New Composite Materials.

E-CAM deliverables D4.2 and D4.3 contain more information on the suite of programs developed under this pilot project.

 

[1] Zhang, G., Moreira, L. A., Stuehn, T., Daoulas, K. C., and Kremer, K., Equilibration of High Molecular Weight Polymer Melts: A Hierarchical Strategy, ACS Macro Lett., 3, 198-203 (2014)

[2] ESPResSo++ is the “Extensible Software Package for Research in Soft Matter based upon C++”, a general-purpose simulation package for soft-matter research, mainly developed at the Max Planck Institute for Polymer Research Mainz. It is freely available under the GNU Public License. http://www.espresso-pp.de/

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Scientific reports from the 2017 E-CAM workshops, are now available on our website

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The scientific reports* from the following workshops conducted in year 2 of the project E-CAM (2017):

  1. E-CAM Scoping Workshop: “From the Atom to the Material” , 18- 20 September 2017, University of Cambridge, UK,
  2. E-CAM State-of-the-Art Workshop WP4: Meso and Multiscale Modelling, 29 May – 1 June 2017, University College Dublin, Ireland,

are now available for download on our website at this location. Furthermore, they will also integrate the CECAM Report of Activities 2017, published every year on the website www.cecam.org.

Each report includes:

  • an overview of the remit of the workshop,
  • the workshop program,
  • the list of attendees,
  • the major outcomes,
  • how these outcomes relate to community needs,
  • how the recommendation could be funded,
  • and how they relate to society and industry,
  • emphasis and impact on software development.

 

*© CECAM 2017, all rights reserved.

Please address any comments or questions to info@e-cam2020.eu.

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New publication using the GC-AdResS molecular dynamics technique

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The publication “Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique (GC-AdResS)“ by the Theoretical and Mathematical Physics in Molecular Simulation group of the Freie Universität Berlin, lead by Prof.Luigi Delle Site, E-CAM partner, describes the use of the GC-AdResS molecular dynamics technique to test the spatial locality of the ionic liquid 1-ethyl 3-methyl imidazolium chloride liquid. The main aspect of GC-AdResS is the possibility to couple two simulation boxes together and combine the advantages of classical atomistic simulations with those from coarse gained simulations.

The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher AIP version can be found at http://aip.scitation.org/doi/10.1063/1.5009066.

E-CAM currently runs a pilot project on the development of the GC-AdResS scheme and one of its goals is to develop a library or recipe with which GC-AdResS can be implemented in any MD Code. The current focus is to adjust the implemented version of GC-AdResS in GROMACS. The long-term goal of this project is to promote and stimulate the community to use it as a tool for multiscale simulations and analysis. More information about this pilot project can be found here.

Article

Title: Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique

Authors:  B. Shadrack Jabes, C. Krekeler, R. Klein and L. Delle Site

Abstract: We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.

The Journal of Chemical Physics 148, 193804 (2018)
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