E-CAM Stories

Interviews, opinion pieces, success stories and case studies from E-CAM.

  • Issue 16 – April 2021

    Issue 16 – April 2021

    E-CAM Newsletter of April 2021   Get the latest news from E-CAM, sign up for our  newsletter.
  • Challenges to Industry of drug substance development

    Challenges to Industry of drug substance development

      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 …
  • Development of an HTC-based, scalable committor analysis tool in OpenPathSampling opens avenues to investigate enzymatic mechanisms linked to Covid-19

    Development of an HTC-based, scalable committor analysis tool in OpenPathSampling opens avenues to investigate enzymatic mechanisms linked to Covid-19

    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 …
  • Proof of concept : recognition as a disruptive technology

    Proof of concept : recognition as a disruptive technology

      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: …
  • Implementation of High-Dimensional Neural Network Potentials

    Implementation of High-Dimensional Neural Network Potentials

      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 …
  • Another successful online training event !

    Another successful online training event !

      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 …
  • Issue 15 – December 2020

    Issue 15 – December 2020

    E-CAM Newsletter of December 2020   Get the latest news from E-CAM, sign up for our  newsletter.
  • Proof of concept  : Metamorphosis

    Proof of concept : Metamorphosis

      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.
  • LearnHPC: dynamic creation of HPC infrastructure for educational purposes

    LearnHPC: dynamic creation of HPC infrastructure for educational purposes

      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 …
  • Comics & Science ? The E-CAM issue: an experiment in dissemination

    Comics & Science ? The E-CAM issue: an experiment in dissemination

      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 …
  • E-CAM article on the EU Research Magazine

    E-CAM article on the EU Research Magazine

      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 …
  • Issue 14 – September 2020

    Issue 14 – September 2020

    E-CAM Newsletter of September 2020   Get the latest news from E-CAM, sign up for our  newsletter.
  • E-CAM Industrial Case Study: Calculations for Applications in Photovoltaic Devices

    E-CAM Industrial Case Study: Calculations for Applications in Photovoltaic Devices

    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, …
  • Addressing interactive HTC workloads with HPC characteristics: introduction to E-CAM’s HTC library

    Addressing interactive HTC workloads with HPC characteristics: introduction to E-CAM’s HTC library

      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 …
  • Accelerating the design and discovery of materials with tailored properties using first principles high-throughput calculations and  automated generation of Wannier functions

    Accelerating the design and discovery of materials with tailored properties using first principles high-throughput calculations and automated generation of Wannier functions

      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 …
  • Issue 13 – April 2020

    Issue 13 – April 2020

    E-CAM Newsletter of April 2020   Get the latest news from E-CAM, sign up for our  newsletter.
  • E-CAM interview with Massimo Noro, Director of Business Development at STFC

    E-CAM interview with Massimo Noro, Director of Business Development at STFC

    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 …
  • Protein based biosensors: application in detecting influenza

    Protein based biosensors: application in detecting influenza

    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 …
  • E-CAM Case Study: The development of the GC-AdResS scheme:

    E-CAM Case Study: The development of the GC-AdResS scheme:

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

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

      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 …
  • Mesoscale simulation of billion atom complex systems using thousands of GPGPU’s, an industry success story

    Mesoscale simulation of billion atom complex systems using thousands of GPGPU’s, an industry success story

    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 …
  • Software vendor SMEs as a boost for technology transfer in industrial simulative pipelines

    Software vendor SMEs as a boost for technology transfer in industrial simulative pipelines

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

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

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

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

    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 …
  • E-CAM Case Study: Designing control pulses for superconducting qubit systems with local control theory

    E-CAM Case Study: Designing control pulses for superconducting qubit systems with local control theory

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

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

    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 simulation of metal ions in protein-water systems using machine learning: An E-CAM case study and conversation

    The simulation of metal ions in protein-water systems using machine learning: An E-CAM case study and conversation

      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 …
  • From Rational Design of Molecular Biosensors to Patent and potential Start-up

    From Rational Design of Molecular Biosensors to Patent and potential Start-up

      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 …
  • A Conversation on Neural Networks, from Polymorph Recognition to Acceleration of Quantum Simulations

    A Conversation on Neural Networks, from Polymorph Recognition to Acceleration of Quantum Simulations

      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, …
  • Rare events, path sampling and the OpenPathSampling package

    Rare events, path sampling and the OpenPathSampling package

      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 …
  • Does our simulation community need EXASCALE ?

    Does our simulation community need EXASCALE ?

    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, …
  • Technology transfer from the academic world to industry is a difficult process in all scientific fields

    Technology transfer from the academic world to industry is a difficult process in all scientific fields

    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 …
  • High Performance Computing, Computer Simulation, and Theoretical Physics: Evolution or Revolution?

    High Performance Computing, Computer Simulation, and Theoretical Physics: Evolution or Revolution?

    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 …
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