GC-AdResS is a technique that speeds up computations without loss of accuracy for key system properties by dividing the simulation box into two or more regions having different levels of resolution, for instance a high resolution region where the molecules of the system are treated at an atomistic level of detail, and other regions where molecules are treated at a coarse grained level, and transition regions where a weighted average of the two resolutions is used. The goal of the E-CAM GC-AdResS pilot project was to eliminate the need of a transition region so as to significantly improve performance, and to allow much greater flexibility. For example, the low resolution region can be a particle reservoir (ranging in detail from coarse grained to ideal gas particles) and a high resolution atomistic region with no transition region, as was needed hitherto. The only requirement is that the two regions can exchange particles, and that a corresponding “thermodynamic” force is computed self-consistently, which it turns out is very simple to implement.
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)
Dr. Jony Castagna, Science and Technology Facilities Council, United Kingdom
Jony Castagna recounts his transition from industry scientist to research software developer at the STFC, his E-CAM rewrite of DL_MESO allowing the simulation of billion atom systems on thousands of GPGPUs, and his latest role as Nvidia ambassador focused on machine learning.
The E-CAM Scoping Workshop “Building the bridge between theories and software: SME as a boost for technology transfer in industrial simulative pipelines”, organised in May 2018 at the Fondazione Istituto Italiano di Tecnologia (IIT), Genoa, brought together top-level scientists of the E-CAM community with expertise in statistical mechanics, multi-scale modeling and electronic structure, and representatives of pharmaceutical and material industries, with the objective to identify the major gaps which still hamper a systematic exploitation of accurate computer simulations in industrial R&D. Special attention was given to the role of SMEs devoted to simulative software development, and several software vendor SMEs were present at the meeting.
The meeting highlighted the role of software vendor SMEs as a key link for the uptake of modelling in industry. They can play an increasingly important role not only in translating the science developed in academia into a proper technological transfer process, but also in building a scientific bridge between the industry requirements in terms of automation and the new theories and algorithms developed at an academic level. There was also a consensus that EU funded Centers of Excellence for Computing Applications, such as E-CAM, can provide an opportunity to enhance the expertise and scope of software vendors SMEs.
Dr. Silvia Chiacchiera, Science and Technology Facilities Council, United Kingdom
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.
With Prof. Tim Conrad (TC), Free University of Berlin, and Dr. Donal Mackernan (DM), University College Dublin.
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.
Dr. Momir Mališ, École Polytechnique Fédérale de Lausanne, Switzerland
A quantum logic gate is one of the key components of the quantum computer, and designing an effective quantum universal gate is one of the major goals in the development of quantum computers. We have developed a software based on local control theory to design efficient state preparation control pulses for universal quantum gates which drive full population transfer between qubit states.
Dr. Hideki Kobayashi, Max-Planck-Institut für Polymerforschung, Germany
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.
With Dr. Francesco Fracchia, Scuola Normale Superiore di Pisa
Interviewer: Dr. Donal Mackernan, University College Dublin
One quarter to one third of all proteins require metals to function but the description of metal ions in standard force fields is still quite primitive. In this case study and interview an E-CAM project to develop a suitable parameterisation using machine learning is described. The training scheme combines classical simulation with electronic structure calculations to produce a force field comprising standard classical force fields with additional terms for the metal ion-water and metal ion-protein interactions. The approach allows simulations to run as fast as standard molecular dynamics codes, and is suitable for efficient massive parallelism scale-up.
The power of advanced simulation combined with statistical theory , experimental know-how and high performance computing is used to design a protein based molecular switch sensor with remarkable sensitivity and significant industry potential. The sensor technology has applications across commercial markets including diagnostics, immuno-chemistry, and therapeutics.