Computation based methods play a growing role in all stages of accelerated medicine pipelines responding to industry challenges of drug substance development. Abstract APC was created In 2011 by Dr. Mark Barrett and Prof. Brian Glennon of the University College Dublin School of Chemical and Bioprocess Engineering with a …
The E-CAM HPC Centre of Excellence and a PRACE team in Wroclaw have teamed up to develop High Throughput Computing (HTC) based tools to enable the computational investigation of reaction mechanisms in complex systems. These tools might help us gain understanding of enzymatic mechanisms used by the SARS-CoV-2 main protease …
Abstract The transformation of a beautiful idea born via simulation into a commercial opportunity is recognised as a disruptive technology. At the heart of this ongoing story is advanced simulation using massively parallel computation, rare-event methods and genetic engineering. Proof of concept : recognition as a disruptive technology Author: …
Abstract In this conversation with Andreas Singraber, post-doc in E-CAM until last month, we will discover the ensemble of his work to expand the Neural Network Potential (NNP) Package n2p2 and to improve user accessibility to the code via the LAMMPS package. Andreas will talk about new tools that …
Our last Extended Software Development Workshop (ESDW) took place on the 18th-22nd January[1], and given its length (5 days) and it’s nature (theory and hands-on training sessions) it was a real success! “The workshop went very well, participants seem to have enjoyed and they lasted until the end !”, said organiser …
Abstract The transformation of a beautiful idea born via simulation into a commercial opportunity is described as it progresses from proof of concept towards a product. At the heart of this ongoing story is advanced simulation using massively parallel computation and rare-event methods.
Abstract In a newly successful PRACE-ICEI proposal, E-CAM, FocusCoE, HPC Carpentry and EESSI join forces to bring HPC resources to the classroom in a simple, secure and scalable way. Our plan is to reproduce the model developed by the Canadian open-source software project Magic Castle. The proposed solution creates …
The E-CAM issue of Comics & Science has just been released on-line…and it’s just the beginning of the adventure! Identifying exciting and original tools to engage the general public with advanced research is an intriguing and non-trivial challenge for the scientific community. E-CAM decided to try something unusual, and …
An article about E-CAM has just been released with the Autumn edition of the EU Research Magazine. The EU research magazine is Europe’s leader in research dissemination. The piece consists on an interview to Prof. Ignacio Pagonabarraga, E-CAM technical manager, Dr. Sara Bonella, leader of our work-package focused on …
Dr. David Lopez, Universidad de Córdoba, Spain Abstract The need to find easily renewable and environmentally friendly energy sources alternative to the traditional fossil fuels is nowadays a global quest. The solar energy is a promising candidate and organic solar cells (OSCs) have attracted attention. In this collaboration with Merck, …
Abstract Traditionally high-throughput computing (HTC) workloads are looked down upon in the HPC space, however the scientific use case for extreme-scale resources required by coordinated HTC workflows exists. For such cases where there may be thousands of tasks each requiring peta-scale computing, E-CAM has extended the data-analytics framework Dask …
A successful collaboration between the EU H2020 E-CAM and MaX Centres of Excellence, and the Swiss NCCR MARVEL Abstract In a recent paper[1], researchers from the Centres of Excellence E-CAM[2] and MaX[3], and the centre for Computational Design and Discovery of Novel Materials NCCR MARVEL[4], have proposed a new …
In 2019, Massimo Noro was invited by the CECAM Headquarters at EPFL (E-CAM coordinator) to give a lecture in the framework of the CECAM/MARVEL Mary Ann Mansigh Conversation Series, entitled “Computer modelling for industrial applications”. E-CAM interviewed Massimo Noro at that occasion. Particularly active in applying atomistic and coarse-grained simulations …
Donal MacKernan, University College Dublin & E-CAM An E-CAM transverse action is the development of a protein based sensor (pending patent filled in by UCD[1,2]) with applications in medical diagnostics, scientific visualisation and therapeutics. At the heart of the sensor is a novel protein based molecular switch which allows extremely …
from smooth coupling to a direct interface (abrupt) Dr. Christian Krekeler, Freie Universität Berlin Abstract 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 …
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 …
Dr. Jony Castagna, Science and Technology Facilities Council, United Kingdom Abstract 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 …
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 …
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 …
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 …
Dr. Momir Mališ, École Polytechnique Fédérale de Lausanne, Switzerland Abstract 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 …
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 …
With Dr. Francesco Fracchia, Scuola Normale Superiore di Pisa Interviewer: Dr. Donal Mackernan, University College Dublin Abstract 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 …
Dr. Donal Mackernan, University College Dublin Abstract 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 …
With Prof. Christoph Dellago (CD), University of Vienna, and Dr. Donal Mackernan (DM), University College Dublin. Abstract Recently there has been a dramatic increase in the use of machine learning in physics and chemistry, including its use to accelerate simulations of systems at an ab-initio level of accuracy, …
In the last few years, modelling of rare events has made tremendous progress and several computational methods have been put forward to study these events. Despite this effort, new approaches have not yet been included, with adequate efficiency and scalability, in common simulation packages. One objective of the Classical …
By Prof. David Ceperley, University of Illinois Urbana-Champaign The computer simulation of electrons, atoms, molecules, and their assemblies in soft and hard matter is foundational for many scientific disciplines and important commercially. Exascale computing is coming and our community should take part as are our colleagues in lattice gauge theory, …
By Prof. Mike Payne, University of Cambridge In many countries there is increasing demand for measurable socio-economic impact from academic research. Perhaps the UK is furthest down this path with a significant fraction of the funding for Universities dependent on the ‘Impact’ (defined as impact outside of academia) of the …
By Prof. Giovanni Ciccotti, University of Rome La Sapienza Numerical physics, i.e. numerical calculations serving the needs of traditional theoretical physics, exists at least since the times of Galileo, and probably long before. As Computer Simulation (started with solving problems in Statistical Mechanics), it exists only since the end of …
